I'm building a somatic variant calling pipeline with snakemake. The pipeline is hosted on Github, and I'd like to use Travis CI for continuous integration testing. Due to privacy concerns, I am looking for a publicly available tumor-normal dataset similar to Genome in a Bottle's NA12878 dataset that I can place online without privacy concerns and use for integration testing. Any sources to find tumor-normal FASTQ data that is publicly available?

  • $\begingroup$ Are you after whole exome sequencing (WES) or whole genome sequencing (WGS) for you variant calling pipeline? $\endgroup$ Jan 9, 2020 at 20:53
  • $\begingroup$ Right now the pipeline only supports WES data, but I'm planning to add WGS support so both data types are of interest! $\endgroup$ Jan 9, 2020 at 23:17
  • $\begingroup$ If the site from the suggested duplicate above doesn't work, do try emailing the study's authors. I did so last year and they were incredibly helpful and actually put the site back up for me! If that isn't possible, leave me a comment here (use @terdon) and I can try and get the data to you. $\endgroup$
    – terdon
    Jan 10, 2020 at 11:44